Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000907.1 Hibiscus syriacus cultivar Beakdansim tig00001799_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 656280
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:368002 original size:22 final size:22
Alignment explanation
Indices: 367936--368002 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
367926 GGCATGTGAA
*
367936 ATATGTCTCGAAGGACCTATGC
1 ATATGTCTCGAAGGACCTATGT
* * *
367958 ATGTGTCCCGAAGGACCTGTGT
1 ATATGTCTCGAAGGACCTATGT
*
367980 ATATGTCTCGAAGGACCTCTGT
1 ATATGTCTCGAAGGACCTATGT
368002 A
1 A
368003 ACCCTTGACT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (22 bp):
ATATGTCTCGAAGGACCTATGT
Found at i:369770 original size:36 final size:35
Alignment explanation
Indices: 369729--369833 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 35
369719 TAGGAAAATA
* *
369729 TCTCAAGCAAGACAAAATTTGTTTTGAGAGAAATTG
1 TCTCAAGCGAGACAAAATTTGTTTTGAGA-AAACTG
* *
369765 TCTCAAGCGAGACAAAATTTGTTTTTAGATAACTG
1 TCTCAAGCGAGACAAAATTTGTTTTGAGAAAACTG
* * *
369800 TCTCAAGCGAGAAAAAATTTATTTTTAGTAAAAC
1 TCTCAAGCGAGACAAAATTTGTTTTGAG-AAAAC
369834 ACCCTCAAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 30 0.49
36 31 0.51
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (35 bp):
TCTCAAGCGAGACAAAATTTGTTTTGAGAAAACTG
Found at i:369809 original size:35 final size:36
Alignment explanation
Indices: 369729--369827 Score: 137
Period size: 35 Copynumber: 2.8 Consensus size: 36
369719 TAGGAAAATA
* * *
369729 TCTCAAGCAAGACAAAATTTGTTTTGAGAGAAATTG
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAACTG
*
369765 TCTCAAGCGAGACAAAATTTGTTTTTAGA-TAACTG
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAACTG
* *
369800 TCTCAAGCGAGAAAAAATTTATTTTTAG
1 TCTCAAGCGAGACAAAATTTGTTTTTAG
369828 TAAAACACCC
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 30 0.53
36 27 0.47
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.33
Consensus pattern (36 bp):
TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAACTG
Found at i:370168 original size:16 final size:16
Alignment explanation
Indices: 370147--370181 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
370137 TTAATGTGTC
* *
370147 ATGTATGTGTTGATGT
1 ATGTATATGTTGATAT
370163 ATGTATATGTTGATAT
1 ATGTATATGTTGATAT
370179 ATG
1 ATG
370182 AGGGAACTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (16 bp):
ATGTATATGTTGATAT
Found at i:373654 original size:14 final size:14
Alignment explanation
Indices: 373624--373674 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
373614 ATGTACCGTA
* *
373624 AAAATGTAAATAT-
1 AAAATGCAAAAATG
*
373637 AAAATGCAAAAGTG
1 AAAATGCAAAAATG
*
373651 AAAATACAAAAATG
1 AAAATGCAAAAATG
373665 AAAATGCAAA
1 AAAATGCAAA
373675 TGCAACGAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
13 10 0.32
14 21 0.68
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (14 bp):
AAAATGCAAAAATG
Found at i:375134 original size:22 final size:23
Alignment explanation
Indices: 375104--375146 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
375094 CTGTCATAAC
* *
375104 TATTTTTTTGAAAAA-AATTAAA
1 TATTATTTTAAAAAACAATTAAA
375126 TATTATTTTAAAAAACAATTA
1 TATTATTTTAAAAAACAATTA
375147 TGCCTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TATTATTTTAAAAAACAATTAAA
Found at i:375866 original size:2 final size:2
Alignment explanation
Indices: 375859--375884 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
375849 TGATAAATTA
375859 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
375885 TTAAAGTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:379353 original size:3 final size:3
Alignment explanation
Indices: 379345--379409 Score: 58
Period size: 3 Copynumber: 21.0 Consensus size: 3
379335 TTTACCCATT
* * * ** *
379345 TTA TTA TTA TTA TAA TTA TTA TCA TAA TTA TTA TTA AAA TTA TAA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
379394 TATA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA
379410 AAAAATATAT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (3 bp):
TTA
Found at i:379364 original size:12 final size:12
Alignment explanation
Indices: 379347--379407 Score: 77
Period size: 12 Copynumber: 4.9 Consensus size: 12
379337 TACCCATTTT
379347 ATTATTATTATA
1 ATTATTATTATA
*
379359 ATTATTATCATA
1 ATTATTATTATA
*
379371 ATTATTATTAAA
1 ATTATTATTATA
*
379383 ATTATAATATATA
1 ATTATTAT-TATA
379396 TATTATTATTAT
1 -ATTATTATTAT
379408 TAAAAAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
12 28 0.68
13 6 0.15
14 7 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTATTATTATA
Found at i:379410 original size:29 final size:29
Alignment explanation
Indices: 379353--379429 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
379343 TTTTATTATT
379353 ATTATAAT-TATTATCATAATTATTATTAAA
1 ATTATAATATA-TAT-ATAATTATTATTAAA
*
379383 ATTATAATATATATATTATTATTATTAAA
1 ATTATAATATATATATAATTATTATTAAA
*
379412 A-AAT-ATATATATAATAAT
1 ATTATAATATATAT-ATAAT
379430 AATAATAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.19
28 6 0.14
29 15 0.36
30 11 0.26
31 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTATAATATATATATAATTATTATTAAA
Found at i:392199 original size:10 final size:9
Alignment explanation
Indices: 392180--392268 Score: 59
Period size: 8 Copynumber: 10.4 Consensus size: 9
392170 ATGCTTGAAT
392180 AGAAGAAAA
1 AGAAGAAAA
392189 AGAAGGAAAA
1 AGAA-GAAAA
* *
392199 AAAAG-AAG
1 AGAAGAAAA
392207 AGAA-AAAA
1 AGAAGAAAA
392215 A-AAGAAAA
1 AGAAGAAAA
*
392223 AGAA-AAAG
1 AGAAGAAAA
392231 AGAA-AAAA
1 AGAAGAAAA
392239 GAGAA-AAGAA
1 -AGAAGAA-AA
*
392249 AAAAG-AAA
1 AGAAGAAAA
392257 A-AAGAAAA
1 AGAAGAAAA
392265 AGAA
1 AGAA
392269 AAAGGGGGGT
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
7 5 0.08
8 30 0.47
9 19 0.30
10 10 0.16
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AGAAGAAAA
Found at i:392211 original size:14 final size:13
Alignment explanation
Indices: 392180--392272 Score: 77
Period size: 14 Copynumber: 7.0 Consensus size: 13
392170 ATGCTTGAAT
*
392180 AGAAGAAAAAGAAG
1 AGAA-AAAAAAAAG
392194 -GAAAAAAAAGAAG
1 AGAAAAAAAA-AAG
392207 AG-AAAAAAAAAG
1 AGAAAAAAAAAAG
*
392219 A-AAAAGAAAAAG
1 AGAAAAAAAAAAG
392231 AGAAAAAAGAGAAA-
1 AGAAAAAA-A-AAAG
*
392245 AGAAAAAAGAAAAA
1 AGAAAAAA-AAAAG
392259 AGAAAAAGAAAAAG
1 AGAAAAA-AAAAAG
392273 GGGGGTCAAG
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
12 19 0.28
13 21 0.31
14 23 0.34
15 4 0.06
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAG
Found at i:392212 original size:24 final size:23
Alignment explanation
Indices: 392183--392262 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 23
392173 CTTGAATAGA
392183 AGAAAAAGAAGGAAAAAAAAGAAG
1 AGAAAAAGAAGGAAAAAAAA-AAG
* *
392207 AGAAAAAAAAAGAAAAAGAAAAAG
1 AGAAAAAGAAGGAAAAA-AAAAAG
392231 AG-AAAA-AAGAGAAAAGAAAAAAG
1 AGAAAAAGAAG-GAAAA-AAAAAAG
392254 A-AAAAAGAA
1 AGAAAAAGAA
392263 AAAGAAAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
22 2 0.04
23 20 0.42
24 23 0.48
25 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (23 bp):
AGAAAAAGAAGGAAAAAAAAAAG
Found at i:392224 original size:6 final size:6
Alignment explanation
Indices: 392182--392272 Score: 77
Period size: 6 Copynumber: 15.5 Consensus size: 6
392172 GCTTGAATAG
*
392182 AAGAAA AAG--A AGGAAA AA-AAA GAAGAGAA AA-AAA AAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA -AAGA-AA AAGAAA AAGAAA AAGAAA
* *
392228 AAGAGA AA-AAA GAG-AA AAGAAAA AAGAAAA AAGAAA AAGAAA AAG
1 AAGAAA AAGAAA AAGAAA AAG-AAA AAG-AAA AAGAAA AAGAAA AAG
392273 GGGGGTCAAG
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
4 3 0.04
5 14 0.20
6 36 0.51
7 15 0.21
8 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:392224 original size:21 final size:20
Alignment explanation
Indices: 392185--392271 Score: 106
Period size: 21 Copynumber: 4.2 Consensus size: 20
392175 TGAATAGAAG
*
392185 AAAAAGAAGGAAA-AAAAAGA
1 AAAAAGAA-AAAAGAAAAAGA
392205 AGAGAAA-AAAAAAGAAAAAGA
1 A-A-AAAGAAAAAAGAAAAAGA
392226 AAAAGAGAAAAAAGAGAAAAGA
1 AAAA-AGAAAAAAGA-AAAAGA
392248 AAAAAGAAAAAAGAAAAAGA
1 AAAAAGAAAAAAGAAAAAGA
392268 AAAA
1 AAAA
392272 GGGGGGTCAA
Statistics
Matches: 60, Mismatches: 1, Indels: 12
0.82 0.01 0.16
Matches are distributed among these distances:
19 2 0.03
20 16 0.27
21 29 0.48
22 13 0.22
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAAAGAAAAAGA
Found at i:392229 original size:7 final size:7
Alignment explanation
Indices: 392197--392271 Score: 93
Period size: 7 Copynumber: 10.7 Consensus size: 7
392187 AAAGAAGGAA
392197 AAAAAAG
1 AAAAAAG
392204 AAGAGAAA-
1 AA-A-AAAG
392212 AAAAAAG
1 AAAAAAG
392219 -AAAAAG
1 AAAAAAG
392225 AAAAAGAG
1 AAAAA-AG
392233 AAAAAAG
1 AAAAAAG
*
392240 AGAAAAG
1 AAAAAAG
392247 AAAAAAG
1 AAAAAAG
392254 AAAAAAG
1 AAAAAAG
392261 -AAAAAG
1 AAAAAAG
392267 AAAAA
1 AAAAA
392272 GGGGGGTCAA
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
6 15 0.25
7 32 0.53
8 10 0.17
9 3 0.05
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:392251 original size:36 final size:38
Alignment explanation
Indices: 392185--392271 Score: 66
Period size: 35 Copynumber: 2.4 Consensus size: 38
392175 TGAATAGAAG
392185 AAAAAGAAG-GAAAAAAAAGAAGAGAAA-AAAAA-AGAAA
1 AAAAAGAAGAGAAAAAAAAGAA-A-AAAGAAAAAGAGAAA
*
392222 AAGAAA-AAGAG--AAAAAAGAGAAAAGAAAAA-AGAAA
1 AA-AAAGAAGAGAAAAAAAAGAAAAAAGAAAAAGAGAAA
392257 AAAGAA-AA-AGAAAAA
1 AAA-AAGAAGAGAAAAA
392272 GGGGGGTCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
34 6 0.14
35 17 0.40
36 11 0.26
37 5 0.12
38 4 0.09
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (38 bp):
AAAAAGAAGAGAAAAAAAAGAAAAAAGAAAAAGAGAAA
Found at i:395000 original size:227 final size:226
Alignment explanation
Indices: 394528--395410 Score: 1214
Period size: 215 Copynumber: 3.9 Consensus size: 226
394518 TAGCAAAGAT
* * * *
394528 TCAAATCCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATC
1 TCAAATCCATCATTTGATGGATCAGCTTTGCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATC
* ** *
394593 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTAAATTCATCAAT
63 TGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATT
* * * * *
394658 TGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAA
128 TGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAA
*
394723 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
190 AAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** *
394760 TTGAATTCATCATTTGATGGATCAGCTTTGCCAGAG-AGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTG
* * * *
394824 AAGAAGGAAGAAAAAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTC
65 AAGAAGGAAG-AAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTT
* *
394889 AATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAG
129 GATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAG
*
394954 TTCATAATAAGAAGAATTTGTTCAACCTTTTGC
194 TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
**
394987 TCAAATCCATCATTCAATGGATCAGCTTTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCT--
1 TCAAATCCATCATTTGATGGATCAGCTTTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* *
395050 --------GAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CTTTTGCTTGAATTCATCATTTGA
66 AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGA
*
395106 TGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTT
131 TGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTT
395171 CATAATGAGAAGAATTTGTTCAACCTTTTGC
196 CATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * *
395202 CCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTAA
1 TCAAATCCATCATTTGATGGATCAGCTTTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* *
395267 AGAATGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGA
66 AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGA
** * * * *
395332 TGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGT
131 TGGATCAGCTTTTCCAG-TTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGT
395397 TCATAATGAGAAGA
195 TCATAATGAGAAGA
395411 GCTTATTTAA
Statistics
Matches: 584, Mismatches: 52, Indels: 35
0.87 0.08 0.05
Matches are distributed among these distances:
215 170 0.29
216 29 0.05
217 1 0.00
225 31 0.05
226 42 0.07
227 164 0.28
228 1 0.00
229 17 0.03
230 81 0.14
232 47 0.08
233 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (226 bp):
TCAAATCCATCATTTGATGGATCAGCTTTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGA
TGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTT
CATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:395002 original size:113 final size:113
Alignment explanation
Indices: 394530--395410 Score: 1136
Period size: 113 Copynumber: 7.8 Consensus size: 113
394520 GCAAAGATTC
* * * * * * *
394530 AAATCCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
1 AAATTCATCATTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAA--C-TCATCTG
* **
394595 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTT
63 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTT
* * * * * *
394646 AAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
1 AAATTCATCATTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAA--C-TCATCTG
*
394711 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
63 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTT
* * **
394762 GAATTCATCATTTGATGGATCAGCTTTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
394827 AAGGAAGAAAAAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAG-AAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTT
* ** *
394876 AAATCCATCATTCAATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
394941 AAGGAAGAAAAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTT
* ** * *
394989 AAATCCATCATTCAATGGATCAGCTTTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCT----
1 AAATTCATCATTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
395050 ------GAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTT
* *
395091 GAATTCATCATTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * **
395156 AAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCC
66 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTT
* * * *
395204 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTAAAG
1 AAATTCATCATTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
395269 AATGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTT
* ** *
395317 GAATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCATTTGATGGATCAGCTTTTCCAG-TTAGAGTTCATAATGAGAAGAACTCATCTGAA
* * *
395382 GGAGAAAGAAGAAGTTCATAATGAGAAGA
65 GAAGGAAGAAGAAGTTCATAATAAGAAGA
395411 GCTTATTTAA
Statistics
Matches: 691, Mismatches: 61, Indels: 28
0.89 0.08 0.04
Matches are distributed among these distances:
102 62 0.09
103 30 0.04
112 29 0.04
113 255 0.37
114 155 0.22
116 160 0.23
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
AAATTCATCATTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTT
Found at i:399315 original size:2 final size:2
Alignment explanation
Indices: 399310--399334 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
399300 AAGTCTTTTG
399310 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
399335 TTAAGATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:403744 original size:156 final size:156
Alignment explanation
Indices: 403453--403769 Score: 618
Period size: 156 Copynumber: 2.0 Consensus size: 156
403443 ACCACCACAT
403453 TTTCTTACAATTAATATCCAGTACAATATAATTACTGCTTATGTATAACATGTTCAGTACAACTT
1 TTTCTTACAATTAATATCCAGTACAATATAATTACTGCTTATGTATAACATGTTCAGTACAACTT
403518 TCACAGGCTAATTTTGTGAAAAGCCCCTTTTTAGTTAATTTTCTGTATATTTGGTAGATGAGAAG
66 TCACAGGCTAATTTTGTGAAAAGCCCCTTTTTAGTTAATTTTCTGTATATTTGGTAGATGAGAAG
403583 CTTAGACTAATCAGGAATACGTTAGG
131 CTTAGACTAATCAGGAATACGTTAGG
403609 TTTCTTACAATTAATATCCAGTACAATATAATTACTGCTTATGTATAACATGTTCAGTACAACTT
1 TTTCTTACAATTAATATCCAGTACAATATAATTACTGCTTATGTATAACATGTTCAGTACAACTT
403674 T-ACAGGCTAATTTTGTGAAAAGCCCCTTTTTAGTTAATTTTCTGTATATTTGGTAGATGAGAAG
66 TCACAGGCTAATTTTGTGAAAAGCCCCTTTTTAGTTAATTTTCTGTATATTTGGTAGATGAGAAG
403738 CTTTAGACTAATCAGGAATACGTTAGG
131 C-TTAGACTAATCAGGAATACGTTAGG
403765 TTTCT
1 TTTCT
403770 AAACTGCCAA
Statistics
Matches: 160, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
155 64 0.40
156 96 0.60
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (156 bp):
TTTCTTACAATTAATATCCAGTACAATATAATTACTGCTTATGTATAACATGTTCAGTACAACTT
TCACAGGCTAATTTTGTGAAAAGCCCCTTTTTAGTTAATTTTCTGTATATTTGGTAGATGAGAAG
CTTAGACTAATCAGGAATACGTTAGG
Found at i:416711 original size:2 final size:2
Alignment explanation
Indices: 416704--416734 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
416694 CCATATTACT
416704 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
416735 TGAGTATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:419049 original size:20 final size:20
Alignment explanation
Indices: 419024--419061 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
419014 AAGTGTAATG
419024 TATACTTATATACATATATC
1 TATACTTATATACATATATC
*
419044 TATACTTATATATATATA
1 TATACTTATATACATATA
419062 AAGTAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TATACTTATATACATATATC
Found at i:419432 original size:2 final size:2
Alignment explanation
Indices: 419427--419471 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
419417 ACTCATGTAA
419427 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
419470 AT
1 AT
419472 TATTTATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:419592 original size:11 final size:11
Alignment explanation
Indices: 419578--419604 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
419568 AGTTAAATTA
419578 TATTAATTAAT
1 TATTAATTAAT
419589 TATTAATTAAT
1 TATTAATTAAT
419600 TATTA
1 TATTA
419605 CATAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTAATTAAT
Found at i:419851 original size:18 final size:18
Alignment explanation
Indices: 419828--419865 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
419818 TATAAATTCA
*
419828 AAATCTCATAACTTCGTC
1 AAATCTCATAACTTCATC
419846 AAATCTCATAACTTCATC
1 AAATCTCATAACTTCATC
419864 AA
1 AA
419866 TTGTAACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (18 bp):
AAATCTCATAACTTCATC
Found at i:419955 original size:16 final size:16
Alignment explanation
Indices: 419936--419966 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
419926 GGTTTAGTCA
419936 ATTACAAATCAGGTTT
1 ATTACAAATCAGGTTT
*
419952 ATTACATATCAGGTT
1 ATTACAAATCAGGTT
419967 GATAACAGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (16 bp):
ATTACAAATCAGGTTT
Found at i:421587 original size:42 final size:43
Alignment explanation
Indices: 421484--421612 Score: 138
Period size: 42 Copynumber: 3.1 Consensus size: 43
421474 CAAACGTAGT
* *
421484 AATAGTTATGTACTTTAGTGGC-GTTTTGTTAATAAACGCCGC
1 AATAATTATGTACTTTAGTGGCATTTTTGTTAATAAACGCCGC
* * * *
421526 AATAATCATGTAATATAGTGGCATTTTTG-TAATACACGCCGC
1 AATAATTATGTACTTTAGTGGCATTTTTGTTAATAAACGCCGC
* * * * *
421568 CATATTTATGTTCTTTAGTGGCATTTTTATT-ATAAATGCCGC
1 AATAATTATGTACTTTAGTGGCATTTTTGTTAATAAACGCCGC
421610 AAT
1 AAT
421613 TCTGCAATCC
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
42 63 0.91
43 6 0.09
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.40
Consensus pattern (43 bp):
AATAATTATGTACTTTAGTGGCATTTTTGTTAATAAACGCCGC
Found at i:425563 original size:30 final size:30
Alignment explanation
Indices: 425516--425601 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 30
425506 CAATATTCTA
* *
425516 AGCTTTGCTAAGCTTTACTCAATTCTCTCT
1 AGCTTTTCTAAGTTTTACTCAATTCTCTCT
*
425546 ATCTTTTCTAAGTTTTACTCAATTCTCTCT
1 AGCTTTTCTAAGTTTTACTCAATTCTCTCT
*
425576 AGCTTTTCTAAGCTTTCACTC-ATTCT
1 AGCTTTTCTAAG-TTTTACTCAATTCT
425602 TATTTTTCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
30 43 0.86
31 7 0.14
ACGTcount: A:0.20, C:0.26, G:0.07, T:0.48
Consensus pattern (30 bp):
AGCTTTTCTAAGTTTTACTCAATTCTCTCT
Found at i:429334 original size:42 final size:41
Alignment explanation
Indices: 429271--429359 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 41
429261 ATTTTGCGGT
*
429271 GTTTGTTAAAAATGCCGCTATAGATATAGACCTTTTGCAAC
1 GTTTGTAAAAAATGCCGCTATAGATATAGACCTTTTGCAAC
* * * *
429312 GTTTGTAAACAAATGTCGCTATATATATCGACCTTTTGCGAC
1 GTTTGTAAA-AAATGCCGCTATAGATATAGACCTTTTGCAAC
429354 GTTTGT
1 GTTTGT
429360 TCCAAAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 8 0.19
42 34 0.81
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (41 bp):
GTTTGTAAAAAATGCCGCTATAGATATAGACCTTTTGCAAC
Found at i:429390 original size:43 final size:43
Alignment explanation
Indices: 429245--429507 Score: 248
Period size: 43 Copynumber: 6.2 Consensus size: 43
429235 CCAAAAAATA
* * ** *
429245 CCGCTATATACAT-GACATTTTGCGGTGTTTGTT--AAAAATG
1 CCGCTATATATATCGACCTTTTGCGACGTTTGTTCCAAAAACG
* * * * *
429285 CCGCTATAGATATAGACCTTTTGCAACGTTTG-T-AAACAAATG
1 CCGCTATATATATCGACCTTTTGCGACGTTTGTTCCAA-AAACG
* *
429327 TCGCTATATATATCGACCTTTTGCGACGTTTGTTCCAAAAAAG
1 CCGCTATATATATCGACCTTTTGCGACGTTTGTTCCAAAAACG
* * * * * *
429370 CGGCTATCTATCTCGACCTTTTGTGGCGTTTGTTCCAAAAACT
1 CCGCTATATATATCGACCTTTTGCGACGTTTGTTCCAAAAACG
* * *
429413 CCGCTATATATCTCGACCTTTTGCGATGCTTGTTCCAAAAACG
1 CCGCTATATATATCGACCTTTTGCGACGTTTGTTCCAAAAACG
* * * *
429456 CCGCTATGTATATCAACCTTTTGTGGCGTTTGTTCCAAAAACG
1 CCGCTATATATATCGACCTTTTGCGACGTTTGTTCCAAAAACG
*
429499 CCACTATAT
1 CCGCTATAT
429508 CTCTTCATCT
Statistics
Matches: 182, Mismatches: 36, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
40 12 0.07
41 16 0.09
42 33 0.18
43 119 0.65
44 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (43 bp):
CCGCTATATATATCGACCTTTTGCGACGTTTGTTCCAAAAACG
Found at i:446969 original size:196 final size:192
Alignment explanation
Indices: 446630--447018 Score: 676
Period size: 196 Copynumber: 2.0 Consensus size: 192
446620 TTTTTGTGTA
446630 ATCCAGAATCATTTGTGTGTTTTGATGCGTCAATATGGTTTTTTCGATTCAATTACCCTACTGAG
1 ATCCAGAATCATTTGTGTGTTTTGATGCGTCAATATGGTTTTTTCGATTCAATTACCCTACTGAG
446695 AAGACATACACTAAATTTTTGTGGCTAGCCGTTCTGTCATGGATTACTGATTCGGGGACTGATAT
66 AAGACATACACTAAATTTTTGTGGCTAGCCGTTCTGTCATGGATTACTGATTCGGGGACTGATAT
*
446760 CTTATTAATTGATCAGTGATATAATAAAAA-TTATGTTAACATTTATTATCTTTTTTTCCCTT
131 CGTATTAATTGATCAGTGATATAATAAAAATTTATGTTAACA-TTATTATCTTTTTTTCCCTT
446822 ATCCAGAATCATTTGTGTGTTTTGATGCGTCAAAATAT-GTATTTTTCGATTCAATTCACCCTAC
1 ATCCAGAATCATTTGTGTGTTTTGATGCGTC--AATATGGT-TTTTTCGATTCAATT-ACCCTAC
446886 TGAGAAGACATACACTAAATTATTTGTGGCTAGCCGTTCTGTCATGGATTTACTGATTC-GGGAC
62 TGAGAAGACATACACTAAATT-TTTGTGGCTAGCCGTTCTGTCATGGA-TTACTGATTCGGGGAC
*
446950 TGATATCGTATTGATTGATCAGTGATATAATAAAAATTTATGTTAACATTATTATCTTTTTTTCC
125 TGATATCGTATTAATTGATCAGTGATATAATAAAAATTTATGTTAACATTATTATCTTTTTTTCC
447015 CTT
190 CTT
447018 A
1 A
447019 CATGTGCTAC
Statistics
Matches: 188, Mismatches: 2, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
192 31 0.16
193 2 0.01
194 20 0.11
195 28 0.15
196 86 0.46
197 21 0.11
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (192 bp):
ATCCAGAATCATTTGTGTGTTTTGATGCGTCAATATGGTTTTTTCGATTCAATTACCCTACTGAG
AAGACATACACTAAATTTTTGTGGCTAGCCGTTCTGTCATGGATTACTGATTCGGGGACTGATAT
CGTATTAATTGATCAGTGATATAATAAAAATTTATGTTAACATTATTATCTTTTTTTCCCTT
Found at i:447356 original size:21 final size:19
Alignment explanation
Indices: 447300--447364 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
447290 TTTAATTATA
*
447300 TAATATAATTAAAATATTT
1 TAATAAAATTAAAATATTT
* *
447319 TTATAAAACTAAAATATTT
1 TAATAAAATTAAAATATTT
*
447338 TAATTGAAATTATAAATATTT
1 TAA-TAAAATTA-AAATATTT
*
447359 TTATAA
1 TAATAA
447365 TATTTTACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 18 0.50
20 8 0.22
21 10 0.28
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
TAATAAAATTAAAATATTT
Found at i:447504 original size:21 final size:21
Alignment explanation
Indices: 447478--447520 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
447468 TAATTTATGT
447478 ATTGGAGCCAACGAGTATCGG
1 ATTGGAGCCAACGAGTATCGG
447499 ATTGGAGCCAACGAGTATCGG
1 ATTGGAGCCAACGAGTATCGG
447520 A
1 A
447521 ACAAGGTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.19, G:0.33, T:0.19
Consensus pattern (21 bp):
ATTGGAGCCAACGAGTATCGG
Found at i:450390 original size:6 final size:6
Alignment explanation
Indices: 450379--450406 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
450369 TTAGTATTGA
450379 TTTTGG TTTTGG TTTTGG TTTTGG TTTT
1 TTTTGG TTTTGG TTTTGG TTTTGG TTTT
450407 ATTTTAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (6 bp):
TTTTGG
Found at i:455814 original size:29 final size:29
Alignment explanation
Indices: 455743--455807 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
455733 AAGCTTGGAT
455743 GAACAAAGGAAAATACATGGAACATGACA
1 GAACAAAGGAAAATACATGGAACATGACA
*
455772 GAACAAAGGAAAATACATGGAACATGATA
1 GAACAAAGGAAAATACATGGAACATGACA
455801 GAACAAA
1 GAACAAA
455808 TGCAAATGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.57, C:0.12, G:0.20, T:0.11
Consensus pattern (29 bp):
GAACAAAGGAAAATACATGGAACATGACA
Found at i:459786 original size:17 final size:17
Alignment explanation
Indices: 459764--459810 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
459754 ACACCAATAG
459764 GAAAATTCCTTTTTTAT
1 GAAAATTCCTTTTTTAT
459781 GAAAATTCCTTTTTTAT
1 GAAAATTCCTTTTTTAT
* *
459798 TATAATT-CTTTTT
1 GAAAATTCCTTTTT
459811 GAATTCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.57
Consensus pattern (17 bp):
GAAAATTCCTTTTTTAT
Found at i:462132 original size:41 final size:41
Alignment explanation
Indices: 462086--462401 Score: 217
Period size: 41 Copynumber: 7.7 Consensus size: 41
462076 TTCAATCGAG
* * * * *
462086 TTCGATCTTGGCAGCATGTAATAGTTCATCATTCAACTTGA
1 TTCGATCATGGTAGCATGCAATAATTCACCATTCAACTTGA
* * * *
462127 TTCGATAATGTTAGCATGCAATAATTCACCATTCGA-TTCAA
1 TTCGATCATGGTAGCATGCAATAATTCACCATTCAACTT-GA
* * * * * *
462168 TTCAATCATGGAATCATACAATAGTTCATCATTCAACTTGA
1 TTCGATCATGGTAGCATGCAATAATTCACCATTCAACTTGA
*
462209 TTCGATCATGGTAGCATGCAATAATTCACCATTCAA-TTCAA
1 TTCGATCATGGTAGCATGCAATAATTCACCATTCAACTT-GA
* * ** * *
462250 TTC-AGTCATGGTAACATACTGTAGTTCATCATTCAACTTGA
1 TTCGA-TCATGGTAGCATGCAATAATTCACCATTCAACTTGA
* * * * *
462291 TCCGATCATGGTAGAATGCAATAATTCACCACTCGA-TTCAA
1 TTCGATCATGGTAGCATGCAATAATTCACCATTCAACTT-GA
* * * * ** * *
462332 TTCAATCATGGAAGCATACAATAGTTCTTCATTTAATTTGA
1 TTCGATCATGGTAGCATGCAATAATTCACCATTCAACTTGA
* * * *
462373 TTCAATCATGGTAACATGCATTTATTCAC
1 TTCGATCATGGTAGCATGCAATAATTCAC
462402 AAACCAATTC
Statistics
Matches: 203, Mismatches: 64, Indels: 16
0.72 0.23 0.06
Matches are distributed among these distances:
40 7 0.03
41 189 0.93
42 7 0.03
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (41 bp):
TTCGATCATGGTAGCATGCAATAATTCACCATTCAACTTGA
Found at i:462242 original size:82 final size:81
Alignment explanation
Indices: 462105--462401 Score: 423
Period size: 82 Copynumber: 3.6 Consensus size: 81
462095 GGCAGCATGT
* *
462105 AATAGTTCATCATTCAACTTGATTCGATAATGTTAGCATGCAATAATTCACCATTCGATTCAATT
1 AATAGTTCATCATTCAACTTGATTCGATCATGGTAGCATGCAATAATTCACCATTCGATTCAATT
462170 CAATCATGGAATCATAC
66 CAATCATGGAA-CATAC
*
462187 AATAGTTCATCATTCAACTTGATTCGATCATGGTAGCATGCAATAATTCACCATTCAATTCAATT
1 AATAGTTCATCATTCAACTTGATTCGATCATGGTAGCATGCAATAATTCACCATTCGATTCAATT
*
462252 CAGTCATGGTAACATAC
66 CAATCATGG-AACATAC
** * * *
462269 TGTAGTTCATCATTCAACTTGATCCGATCATGGTAGAATGCAATAATTCACCACTCGATTCAATT
1 AATAGTTCATCATTCAACTTGATTCGATCATGGTAGCATGCAATAATTCACCATTCGATTCAATT
462334 CAATCATGGAAGCATAC
66 CAATCATGGAA-CATAC
* * * * * * *
462351 AATAGTTCTTCATTTAATTTGATTCAATCATGGTAACATGCATTTATTCAC
1 AATAGTTCATCATTCAACTTGATTCGATCATGGTAGCATGCAATAATTCAC
462402 AAACCAATTC
Statistics
Matches: 191, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
81 2 0.01
82 187 0.98
83 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (81 bp):
AATAGTTCATCATTCAACTTGATTCGATCATGGTAGCATGCAATAATTCACCATTCGATTCAATT
CAATCATGGAACATAC
Found at i:462352 original size:164 final size:164
Alignment explanation
Indices: 462107--462415 Score: 474
Period size: 164 Copynumber: 1.9 Consensus size: 164
462097 CAGCATGTAA
* * * *
462107 TAGTTCATCATTCAACTTGATTCGATAATGTTAGCATGCAATAATTCACCATTCGATTCAATTCA
1 TAGTTCATCATTCAACTTGATCCGATAATGGTAGAATGCAATAATTCACCACTCGATTCAATTCA
* * *
462172 ATCATGGAATCATACAATAGTTCATCATTCAACTTGATTCGATCATGGTAGCATGCAATAATTCA
66 ATCATGGAAGCATACAATAGTTCATCATTCAACTTGATTCAATCATGGTAACATGCAATAATTCA
* **
462237 CCATTCAATTCAATTCAGTCATGGTAACATACTG
131 CAAACCAATTCAATTCAGTCATGGTAACATACTG
*
462271 TAGTTCATCATTCAACTTGATCCGATCATGGTAGAATGCAATAATTCACCACTCGATTCAATTCA
1 TAGTTCATCATTCAACTTGATCCGATAATGGTAGAATGCAATAATTCACCACTCGATTCAATTCA
* * * * *
462336 ATCATGGAAGCATACAATAGTTCTTCATTTAATTTGATTCAATCATGGTAACATGCATTTATTCA
66 ATCATGGAAGCATACAATAGTTCATCATTCAACTTGATTCAATCATGGTAACATGCAATAATTCA
462401 CAAACCAATTCAATT
131 CAAACCAATTCAATT
462416 TAAATCAAGG
Statistics
Matches: 129, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
164 129 1.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (164 bp):
TAGTTCATCATTCAACTTGATCCGATAATGGTAGAATGCAATAATTCACCACTCGATTCAATTCA
ATCATGGAAGCATACAATAGTTCATCATTCAACTTGATTCAATCATGGTAACATGCAATAATTCA
CAAACCAATTCAATTCAGTCATGGTAACATACTG
Found at i:464236 original size:42 final size:43
Alignment explanation
Indices: 464156--464238 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 43
464146 TCCTTTTTCC
* *
464156 AATTCAATTAATTTAAATGTTCAATTCAATTAGATCTTTATTT
1 AATTCAATTAATTGAAATGCTCAATTCAATTAGATCTTTATTT
* * * *
464199 AATTCCATTAATTGAAAT-CTCTATTCAATTTGGTCTTTAT
1 AATTCAATTAATTGAAATGCTCAATTCAATTAGATCTTTAT
464239 ACTAGGCAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 18 0.53
43 16 0.47
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (43 bp):
AATTCAATTAATTGAAATGCTCAATTCAATTAGATCTTTATTT
Found at i:465120 original size:18 final size:19
Alignment explanation
Indices: 465097--465140 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
465087 AGTTGTTTTA
465097 AAATAAAAG-AAAAGAATT
1 AAATAAAAGAAAAAGAATT
*
465115 AAATAAAAGAAAAATAATT
1 AAATAAAAGAAAAAGAATT
465134 AAATAAA
1 AAATAAA
465141 CAAATTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (19 bp):
AAATAAAAGAAAAAGAATT
Found at i:465862 original size:19 final size:19
Alignment explanation
Indices: 465834--465942 Score: 59
Period size: 19 Copynumber: 5.8 Consensus size: 19
465824 AAATAATATT
*
465834 CTAAATCCTAATTAAAATA
1 CTAAAACCTAATTAAAATA
* *
465853 CTAAAACCTATTTAAACTA
1 CTAAAACCTAATTAAAATA
* *
465872 --AAATACCTAA-AACAAAGA
1 CTAAA-ACCTAATTA-AAATA
**
465890 -TAAAATATAA--AAAATA
1 CTAAAACCTAATTAAAATA
*
465906 TCCTAAAACTTAATTAAAATA
1 --CTAAAACCTAATTAAAATA
*
465927 CTAAAACCTATTTAAA
1 CTAAAACCTAATTAAA
465943 CTAAAATACC
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
16 4 0.06
17 5 0.07
18 12 0.18
19 41 0.60
21 6 0.09
ACGTcount: A:0.57, C:0.15, G:0.01, T:0.28
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:465867 original size:74 final size:74
Alignment explanation
Indices: 465781--465973 Score: 293
Period size: 74 Copynumber: 2.6 Consensus size: 74
465771 ACTTAACACT
* * * * *
465781 TAAAA-CTATTTAAACTAAAATACCTAAAA-AGTA-ATAATATTTAAAATAATATTCTAAATCCT
1 TAAAACCTATTTAAACTAAAATACCTAAAACA-AAGATAAAATATAAAA-AATATCCTAAAACCT
465843 AATTAAAATAC
64 AATTAAAATAC
*
465854 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAAATATCCTAAAACTTAA
1 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAAATATCCTAAAACCTAA
465919 TTAAAATAC
66 TTAAAATAC
465928 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
465974 TGTTTAAAAT
Statistics
Matches: 111, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
73 5 0.05
74 94 0.85
75 12 0.11
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (74 bp):
TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAAATATCCTAAAACCTAA
TTAAAATAC
Found at i:466901 original size:543 final size:535
Alignment explanation
Indices: 466105--467177 Score: 1744
Period size: 543 Copynumber: 2.0 Consensus size: 535
466095 CGTCTTGCAC
* *
466105 AGAAAATGAATGAAAACAAATAATTAAGCCACAAAAACCAATGATTAAGGAATAATTTAAAAGCA
1 AGAAAATGAATGAAAACAAACAATTAAGCCACAAAAACCAATGATTAAGGAAGAATTTAAAAGCA
*
466170 AAATATTAACTAAATTAAGCACTTATCAAATTCCCCCTCACTTATTCAATGCTTGTCCTCATGCA
66 AAATATTAACTAAATTAAGCACTTATCAAATTCCCCCTCACTTATTCAATGCTTGTCCTCAAGCA
* *
466235 TTCATTAATTAACATATCAAAATCATAAGTTGTCATCTATTCCTCAAACTTCCAATCGAACTAAG
131 TTCATCAAATAACATATCAAAATCATAAGTTGTCATCTATTCCTCAAACTTCCAATCGAACTAAG
466300 TCCATGATATTTGTCGAATTCAAGTTACAATCAAGCAAAGATACAACCAAGAAAATTTAAAGTAA
196 TCCATGATATTTGTCGAATTCAAGTTACAATCAAGCAAAGATACAACCAAGAAAATTTAAAGTAA
*
466365 GCAAGATATCACAATTAATTGCCAACTTCAATGAAACATGACTCAATACCTCACAAAGATTAACA
261 GCAAGATATCACAATTAATTGCCAACTTCAACGAAACATGACTCAATACCTCACAAAGATTAACA
* *
466430 TATATCTGCTCAAAGTGTTTGGGGTAAATGAAATCGCTCAAACCGAAACTAACAAAAATATTACC
326 CATATCCGCTCAAAGTGTTTGGGGTAAATGAAATCGCTCAAACCGAAACTAACAAAAATATTACC
* * * *
466495 ATAGGCATGGAATCCAATCAAGTCTCTACTACGAAAAAT-AAACATAATGCAATAATCAAGGGGT
391 ATAGGCATGGAATCCAATCAAGTATCCACTACGAAAAATGAAA-ATAATACAATAATCAAGAGGT
466559 CTTTAAATCAAGGTGTAATGGGGCTTAGGTTAAGGTAGGGAAAAGGCCG-AAA-AAAGGTTTAAA
455 CTTTAAA-CAAGGTGTAATGGGGCTTAGGTTAAGGTAGGGAAAAGGCCGAAAAGAAAGGTTTAAA
466622 ATACTAAAACAATTAAT
519 ATACTAAAACAATTAAT
**
466639 AGAAAATGAATGAAAATGAACAATTAAGCCACAAAAACCAATGATTAAGG-AGAATTTAAAAGCA
1 AGAAAATGAATGAAAACAAACAATTAAGCCACAAAAACCAATGATTAAGGAAGAATTTAAAAGCA
466703 AAATATTAACTAAATTAAGCACTTATCAAATTCCCCCTCACTT-TTCAATGCTTGTCCTCAAGCA
66 AAATATTAACTAAATTAAGCACTTATCAAATTCCCCCTCACTTATTCAATGCTTGTCCTCAAGCA
* * * * *
466767 TTCATCAAATAGCATATCAAAATCATATGTTTCAACTTCAATTTCAATTTATTTCTTAAACTTCC
131 TTCATCAAATAACATATCAAAATCATAAG-TT----GTC-A--TC----TATTCCTCAAACTTCC
* *
466832 AATCGAACTAAGT-CATGATATTTGTTGAATTCAATTTACAATCAAGCAAAGATACAACCAAGAA
184 AATCGAACTAAGTCCATGATATTTGTCGAATTCAAGTTACAATCAAGCAAAGATACAACCAAGAA
466896 AATTTAAAGTAAGCAAGATATCACAATTAATTGCCAACTTCAACGAAACATGACTCAATACCTCA
249 AATTTAAAGTAAGCAAGATATCACAATTAATTGCCAACTTCAACGAAACATGACTCAATACCTCA
*
466961 CAAAGATTAACACATATCCGCTCAAAGTGTTTGGGGTAAATGAAATCGTTCAAACCGAAACTAAC
314 CAAAGATTAACACATATCCGCTCAAAGTGTTTGGGGTAAATGAAATCGCTCAAACCGAAACTAAC
* * *
467026 CAAAATATTACCATAGGCTTGGAATCCAATCAAGTATCCATTACGAAAAATGAAAATAATACAAT
379 AAAAATATTACCATAGGCATGGAATCCAATCAAGTATCCACTACGAAAAATGAAAATAATACAAT
*
467091 AATCAAGAGGTCTTTAAACAAGGTGTAATGGGGCTTAGGTTAGGGTAGGGAAAAGGCCGAAAAGA
444 AATCAAGAGGTCTTTAAACAAGGTGTAATGGGGCTTAGGTTAAGGTAGGGAAAAGGCCGAAAAGA
467156 AAGGTTTAAAATACTAAAACAA
509 AAGGTTTAAAATACTAAAACAA
467178 GAGATCAAAA
Statistics
Matches: 498, Mismatches: 26, Indels: 20
0.92 0.05 0.04
Matches are distributed among these distances:
532 45 0.09
533 58 0.12
534 47 0.09
537 2 0.00
538 1 0.00
540 2 0.00
542 40 0.08
543 250 0.50
544 53 0.11
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (535 bp):
AGAAAATGAATGAAAACAAACAATTAAGCCACAAAAACCAATGATTAAGGAAGAATTTAAAAGCA
AAATATTAACTAAATTAAGCACTTATCAAATTCCCCCTCACTTATTCAATGCTTGTCCTCAAGCA
TTCATCAAATAACATATCAAAATCATAAGTTGTCATCTATTCCTCAAACTTCCAATCGAACTAAG
TCCATGATATTTGTCGAATTCAAGTTACAATCAAGCAAAGATACAACCAAGAAAATTTAAAGTAA
GCAAGATATCACAATTAATTGCCAACTTCAACGAAACATGACTCAATACCTCACAAAGATTAACA
CATATCCGCTCAAAGTGTTTGGGGTAAATGAAATCGCTCAAACCGAAACTAACAAAAATATTACC
ATAGGCATGGAATCCAATCAAGTATCCACTACGAAAAATGAAAATAATACAATAATCAAGAGGTC
TTTAAACAAGGTGTAATGGGGCTTAGGTTAAGGTAGGGAAAAGGCCGAAAAGAAAGGTTTAAAAT
ACTAAAACAATTAAT
Found at i:468390 original size:4 final size:5
Alignment explanation
Indices: 468352--468464 Score: 93
Period size: 5 Copynumber: 21.8 Consensus size: 5
468342 TGTTCAAAGA
* *
468352 AAAAT AAAAT AAAAT TAATT AAAAT AAAAT AAAAT -AAAT AAAAT GAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT
* **** * *
468402 AAAGT TTGCT AAAATAT AAAAT AAAAAT AAAACG AAAAT AAAAT GAAAT
1 AAAAT AAAAT -AAA-AT AAAAT -AAAAT AAAA-T AAAAT AAAAT AAAAT
468451 AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
468465 AAATAGAACG
Statistics
Matches: 85, Mismatches: 17, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
4 4 0.05
5 63 0.74
6 17 0.20
7 1 0.01
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:468475 original size:39 final size:39
Alignment explanation
Indices: 468357--468477 Score: 136
Period size: 39 Copynumber: 3.1 Consensus size: 39
468347 AAAGAAAAAT
* *
468357 AAAATAAAATTAATTAAAATAAAATAAAATAAATAAAATG
1 AAAATAAAATTAAATAAAATAAAATAAAA-AAATAAAACG
* *** *
468397 AAAATAAAGTTTGCTAAAATATAAA-ATAAAAATAAAACG
1 AAAATAAAATTAAATAAAATA-AAATAAAAAAATAAAACG
* *
468436 AAAATAAAATGAAATAAAATAAAATAAAAAAATAGAACG
1 AAAATAAAATTAAATAAAATAAAATAAAAAAATAAAACG
468475 AAA
1 AAA
468478 TGGGTTGCCT
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
38 3 0.05
39 40 0.61
40 20 0.30
41 3 0.05
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (39 bp):
AAAATAAAATTAAATAAAATAAAATAAAAAAATAAAACG
Found at i:474149 original size:18 final size:19
Alignment explanation
Indices: 474128--474171 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
474118 GTTGTTTTTA
*
474128 AAATAAAAG-ATAATAATT
1 AAATAAAAGAAAAATAATT
474146 AAATAAAAGAAAAATAATT
1 AAATAAAAGAAAAATAATT
474165 AAATAAA
1 AAATAAA
474172 CAAATTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AAATAAAAGAAAAATAATT
Found at i:474171 original size:23 final size:23
Alignment explanation
Indices: 474126--474171 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
474116 AAGTTGTTTT
* *
474126 TAAAATAAAAGATAATAATTAAA
1 TAAAAGAAAAGATAATAAATAAA
474149 TAAAAGAAAA-ATAATTAAATAAA
1 TAAAAGAAAAGATAA-TAAATAAA
474172 CAAATTAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (23 bp):
TAAAAGAAAAGATAATAAATAAA
Found at i:474854 original size:12 final size:12
Alignment explanation
Indices: 474837--474863 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
474827 CCTAAAAAGT
474837 AATAATATTTTA
1 AATAATATTTTA
474849 AATAATATTTTA
1 AATAATATTTTA
474861 AAT
1 AAT
474864 CCTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATAATATTTTA
Found at i:474905 original size:74 final size:72
Alignment explanation
Indices: 474781--474996 Score: 254
Period size: 74 Copynumber: 2.9 Consensus size: 72
474771 AAACTAAAAC
* *
474781 ATCTTAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAAAG-TAATAATAT
1 ATCTTAAATCCTAATTAAAATAC-TAAACCTATTTAAACTAAAATACCTAAAAAGATAA-AATA-
**
474845 TTTAAATAAT
63 TAAAAATAAT
* *
474855 ATTTTAAATCCTAATTAAAATACTAAATCCTGTTTAAACTAAAATACCTAAAAAGATAAAATATA
1 ATCTTAAATCCTAATTAAAATACTAAA-CCTATTTAAACTAAAATACCTAAAAAGATAAAATATA
474920 AAAATAAT
65 AAAATAAT
* * * * *
474928 ATCCTAAAACTTAATTAAAATACTAAAACCTATTTAACCTAAAATACATAAAAGAAAGATAAAAT
1 ATCTTAAATCCTAATTAAAATACT-AAACCTATTTAAACTAAAATACCT--AA-AAAGATAAAAT
474993 ATAA
62 ATAA
474997 TGTTTAAAAT
Statistics
Matches: 123, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
73 50 0.41
74 53 0.43
75 5 0.04
76 15 0.12
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (72 bp):
ATCTTAAATCCTAATTAAAATACTAAACCTATTTAAACTAAAATACCTAAAAAGATAAAATATAA
AAATAAT
Found at i:474964 original size:73 final size:73
Alignment explanation
Indices: 474785--474996 Score: 248
Period size: 73 Copynumber: 2.8 Consensus size: 73
474775 TAAAACATCT
* * **
474785 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAAG-TAATAATATTTT
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAAAGATAA-AATA-TAA
**
474848 AAATAATATTT
63 AAATAATATCC
* * *
474859 TAAATCCTAATTAAAATACTAAATCCTGTTTAAACTAAAATACCTAAAAAGATAAAATATAAAAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAGATAAAATATAAAAA
474924 TAATATCC
66 TAATATCC
* * *
474932 TAAAACTTAATTAAAATACTAAAACCTATTTAACCTAAAATACATAAAAGAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT--AA-AAAGATAAAATATAA
474997 TGTTTAAAAT
Statistics
Matches: 120, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
73 53 0.44
74 47 0.39
75 5 0.04
76 15 0.12
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (73 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAGATAAAATATAAAAA
TAATATCC
Found at i:485516 original size:2 final size:2
Alignment explanation
Indices: 485509--485537 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
485499 GCCCATGTTT
485509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
485538 TAGTTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:487622 original size:20 final size:22
Alignment explanation
Indices: 487597--487636 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
487587 CAATTTGGAT
487597 TAGTTCCAA-TAGC-TTTTTTC
1 TAGTTCCAACTAGCATTTTTTC
*
487617 TAGTTCGAACTAGCATTTTT
1 TAGTTCCAACTAGCATTTTT
487637 GGGTACATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 4 0.24
22 5 0.29
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.47
Consensus pattern (22 bp):
TAGTTCCAACTAGCATTTTTTC
Found at i:487635 original size:21 final size:20
Alignment explanation
Indices: 487597--487636 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
487587 CAATTTGGAT
*
487597 TAGTTCCAATAGCTTTTTTC
1 TAGTTCCAATAGCATTTTTC
*
487617 TAGTTCGAACTAGCATTTTT
1 TAGTTCCAA-TAGCATTTTT
487637 GGGTACATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.47
Consensus pattern (20 bp):
TAGTTCCAATAGCATTTTTC
Found at i:491122 original size:19 final size:19
Alignment explanation
Indices: 491098--491155 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
491088 ATTTTATTAT
491098 TTTTTATATGTATATTTAA
1 TTTTTATATGTATATTTAA
*
491117 -TTTT-TA-GT-GATTTAA
1 TTTTTATATGTATATTTAA
* *
491132 TTTTTATTTTTATATTTAA
1 TTTTTATATGTATATTTAA
491151 TTTTT
1 TTTTT
491156 TTTATTTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 6 0.19
16 6 0.19
17 3 0.10
18 5 0.16
19 11 0.35
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTTATATGTATATTTAA
Found at i:491195 original size:37 final size:37
Alignment explanation
Indices: 491129--491199 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
491119 TTTAGTGATT
* * *
491129 TAATTTTTATTTTTATATTTAATTTTTTTTATTTGAA
1 TAATTTTTATTTATATATTTAAATATTTTTATTTGAA
491166 TAATTTTTATTTATA-ATTTAAAATATTTTTATTT
1 TAATTTTTATTTATATATTT-AAATATTTTTATTT
491200 TTTATAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 4 0.13
37 26 0.87
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (37 bp):
TAATTTTTATTTATATATTTAAATATTTTTATTTGAA
Found at i:491337 original size:21 final size:20
Alignment explanation
Indices: 491313--491372 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
491303 TTAACCACCA
*
491313 TGAATTGTCATGTCAGTAACG
1 TGAA-TGTCATGTCAGCAACG
** *
491334 TGAATCACAATGTCAGCACCG
1 TGAATGTC-ATGTCAGCAACG
491355 TGAACTGTCATGTCAGCA
1 TGAA-TGTCATGTCAGCA
491373 TTGTAAAAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (20 bp):
TGAATGTCATGTCAGCAACG
Found at i:491861 original size:19 final size:19
Alignment explanation
Indices: 491837--491902 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
491827 TTAAATCATT
491837 TGATGACGTGATTGACGGA
1 TGATGACGTGATTGACGGA
*
491856 TGATGACGTGATTGACAGA
1 TGATGACGTGATTGACGGA
** *
491875 TGATGATATGACTGACGGA
1 TGATGACGTGATTGACGGA
*
491894 TGTTGACGT
1 TGATGACGT
491903 AGACATATCA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.27, C:0.11, G:0.33, T:0.29
Consensus pattern (19 bp):
TGATGACGTGATTGACGGA
Found at i:498527 original size:18 final size:19
Alignment explanation
Indices: 498490--498527 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
498480 TAAATTTTTT
*
498490 AAAATAAAAAATACTATAA
1 AAAATAAAAAATAATATAA
498509 AAAATAAAAAATAAT-TAA
1 AAAATAAAAAATAATATAA
498527 A
1 A
498528 TTTATGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAATAAAAAATAATATAA
Found at i:501924 original size:29 final size:29
Alignment explanation
Indices: 501871--501930 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 29
501861 CATACTTAGC
*
501871 ATAAAAATAAAACTTGAAAATAAAGA-AAA
1 ATAAAAAT-AAACTTGAAAAAAAAGAGAAA
501900 ATAAAAAT-AACTTGAAAAGGAAAAGAGAAA
1 ATAAAAATAAACTTGAAAA--AAAAGAGAAA
501930 A
1 A
501931 CTTTTATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 10 0.37
29 13 0.48
30 4 0.15
ACGTcount: A:0.70, C:0.03, G:0.12, T:0.15
Consensus pattern (29 bp):
ATAAAAATAAACTTGAAAAAAAAGAGAAA
Found at i:509920 original size:16 final size:17
Alignment explanation
Indices: 509890--509923 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
509880 ACCTTGTCTT
509890 AATAACTAACGAAATAA
1 AATAACTAACGAAATAA
*
509907 AATAA-TAACTAAATAA
1 AATAACTAACGAAATAA
509923 A
1 A
509924 TCACTCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.68, C:0.09, G:0.03, T:0.21
Consensus pattern (17 bp):
AATAACTAACGAAATAA
Found at i:509983 original size:19 final size:19
Alignment explanation
Indices: 509955--510017 Score: 117
Period size: 19 Copynumber: 3.3 Consensus size: 19
509945 GTTTATTTCT
*
509955 AAGTTCGATTTTGAATTCA
1 AAGTTTGATTTTGAATTCA
509974 AAGTTTGATTTTGAATTCA
1 AAGTTTGATTTTGAATTCA
509993 AAGTTTGATTTTGAATTCA
1 AAGTTTGATTTTGAATTCA
510012 AAGTTT
1 AAGTTT
510018 AAATATGGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (19 bp):
AAGTTTGATTTTGAATTCA
Found at i:513442 original size:169 final size:167
Alignment explanation
Indices: 513218--513554 Score: 606
Period size: 169 Copynumber: 2.0 Consensus size: 167
513208 GTTCATATAT
513218 AGTGGCGTATTTAATAATCCACAATAGAGATGTATTTAGCGGCACAACAAATTAGTACTTTAGTG
1 AGTGGCGTATTTAATAATCCACAATAGAGATGTATTTAGCGGCACAACAAATTAGTACTTTAGTG
*
513283 GCTTTTTTTAACAAATGTCGCAATCGAGTTGTATAGCGTC-TTTATAGAGGCATTTTTTGATCAA
66 GCTTTTTTTAACAAATGTCGCAATAGAGTTGTATAGCGTCATTTATAGAGGCATTTTTTGATCAA
513347 ACACCGC-AAAGACTCAGACTTTCATGGCGTTTGTGA
131 ACACCGCAAAAGACTCAGACTTTCATGGCGTTTGTGA
513383 AGTGGCGTATTTATAATAAATCCACAATAGAGATGTATTTTAGCGGCACAACAAATTAGTACTTT
1 AGTGGCGTA-TT-TAAT-AATCCACAATAGAGATGTA-TTTAGCGGCACAACAAATTAGTACTTT
513448 AGTGGCTTTTTTTAACAAATGTCGCAATAGAGTTGTATAGCGTCATTTATAGAGGCATTTTTTGA
62 AGTGGCTTTTTTTAACAAATGTCGCAATAGAGTTGTATAGCGTCATTTATAGAGGCATTTTTTGA
*
513513 TCAAACACCGCAAAAGACTTAGACTTTCATGGCGTTTGTGA
127 TCAAACACCGCAAAAGACTCAGACTTTCATGGCGTTTGTGA
513554 A
1 A
513555 CAAACGCCGC
Statistics
Matches: 164, Mismatches: 2, Indels: 6
0.95 0.01 0.03
Matches are distributed among these distances:
165 9 0.05
166 2 0.01
167 4 0.02
168 19 0.12
169 70 0.43
170 31 0.19
171 29 0.18
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (167 bp):
AGTGGCGTATTTAATAATCCACAATAGAGATGTATTTAGCGGCACAACAAATTAGTACTTTAGTG
GCTTTTTTTAACAAATGTCGCAATAGAGTTGTATAGCGTCATTTATAGAGGCATTTTTTGATCAA
ACACCGCAAAAGACTCAGACTTTCATGGCGTTTGTGA
Found at i:513677 original size:44 final size:44
Alignment explanation
Indices: 513605--513691 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 44
513595 TCAAATGTCG
* * *
513605 CAATAGTCATGTACTTTAGTGGCATTTTTTTTGTAATAAACGCCA
1 CAATAATCATGTAATTAAGTGGCATTTTTTTTGT-ATAAACGCCA
*
513650 CAATAATCATGTAATTAAGTGG-GTTTTTTTTGTATAAACGCC
1 CAATAATCATGTAATTAAGTGGCATTTTTTTTGTATAAACGCC
513692 GTAATAGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 9 0.24
44 10 0.26
45 19 0.50
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (44 bp):
CAATAATCATGTAATTAAGTGGCATTTTTTTTGTATAAACGCCA
Found at i:513705 original size:43 final size:45
Alignment explanation
Indices: 513605--513705 Score: 125
Period size: 43 Copynumber: 2.3 Consensus size: 45
513595 TCAAATGTCG
* *
513605 CAATAGTCATGTACTTTAGTGGCATTTTTTTTGTAATAAACGCCA
1 CAATAGTCATGTAATTAAGTGGCATTTTTTTTGTAATAAACGCCA
* * *
513650 CAATAATCATGTAATTAAGTGG-GTTTTTTTTGT-ATAAACGCCG
1 CAATAGTCATGTAATTAAGTGGCATTTTTTTTGTAATAAACGCCA
* *
513693 TAATAGTTATGTA
1 CAATAGTCATGTA
513706 CCTTAGTGAC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 19 0.40
44 10 0.21
45 19 0.40
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.41
Consensus pattern (45 bp):
CAATAGTCATGTAATTAAGTGGCATTTTTTTTGTAATAAACGCCA
Found at i:513907 original size:21 final size:21
Alignment explanation
Indices: 513854--513912 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
513844 CAAATCGGTG
* *
513854 CACCACTCACCACCGTCGCGC
1 CACCAATCACCACCGTCACGC
* * * *
513875 CATCAGTGACCACCGTTACGC
1 CACCAATCACCACCGTCACGC
*
513896 CACCAATCACCATCGTC
1 CACCAATCACCACCGTC
513913 GTGCCGCCAG
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.47, G:0.14, T:0.15
Consensus pattern (21 bp):
CACCAATCACCACCGTCACGC
Found at i:513970 original size:2 final size:2
Alignment explanation
Indices: 513963--514016 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
513953 TAGTTGTTGC
513963 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
514004 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
514017 TATTAGTGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:515980 original size:19 final size:20
Alignment explanation
Indices: 515955--516002 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 20
515945 ATCATGTTCC
515955 CTGGTAATCTTTTATTCCTA
1 CTGGTAATCTTTTATTCCTA
*
515975 -TGGTAA--TTTTATTCTTA
1 CTGGTAATCTTTTATTCCTA
*
515992 CTGGCAATCTT
1 CTGGTAATCTT
516003 GACATTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
17 10 0.43
18 5 0.22
19 6 0.26
20 2 0.09
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCTA
Found at i:517290 original size:42 final size:41
Alignment explanation
Indices: 517183--517308 Score: 144
Period size: 41 Copynumber: 3.0 Consensus size: 41
517173 GGTAATTAGC
* *
517183 GCGTTGTATCCAAAAACGCTGCTATATATCTGACCTTTTGCG
1 GCGTTGT-TCCAAAAACGCTGCTATAGATCTGACCTTTTACG
* * * *
517225 GTGTTGTTCCATAAACGTTGCTATAGATCTGATCTTTTACG
1 GCGTTGTTCCAAAAACGCTGCTATAGATCTGACCTTTTACG
* * *
517266 GCGTTTGTTCTAAAAACGCCGCTATAGATCTCGACCTATTACG
1 GCG-TTGTTCCAAAAACGCTGCTATAGATCT-GACCTTTTACG
517309 ACATTTTTGT
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 31 0.45
42 29 0.42
43 9 0.13
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (41 bp):
GCGTTGTTCCAAAAACGCTGCTATAGATCTGACCTTTTACG
Found at i:520882 original size:15 final size:16
Alignment explanation
Indices: 520853--520885 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
520843 TTTATATGAG
520853 CATAAGATAACTAAAA
1 CATAAGATAACTAAAA
*
520869 CATAA-ATAATTAAAA
1 CATAAGATAACTAAAA
520884 CA
1 CA
520886 AGGAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.64, C:0.12, G:0.03, T:0.21
Consensus pattern (16 bp):
CATAAGATAACTAAAA
Found at i:521930 original size:16 final size:17
Alignment explanation
Indices: 521899--521931 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
521889 TATTTTAATA
*
521899 TAAAATATATATTAAAT
1 TAAAATATAAATTAAAT
521916 TAAAA-ATAAATTAAAT
1 TAAAATATAAATTAAAT
521932 AAATTAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATATAAATTAAAT
Found at i:522182 original size:24 final size:22
Alignment explanation
Indices: 522131--522182 Score: 52
Period size: 23 Copynumber: 2.2 Consensus size: 22
522121 CATTAAAATT
522131 AAATATATTAATAGTTTTAAAAA
1 AAATATATTAATAG-TTTAAAAA
*
522154 TAATATACTTAATAAG-TTAAAACA
1 AAATATA-TTAAT-AGTTTAAAA-A
522178 AAATA
1 AAATA
522183 AAAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 12 0.50
24 10 0.42
25 2 0.08
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (22 bp):
AAATATATTAATAGTTTAAAAA
Found at i:526309 original size:17 final size:17
Alignment explanation
Indices: 526285--526323 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
526275 AATAGTAAGT
*
526285 AAAAATAAATAATAAA-
1 AAAAATAAAAAATAAAG
526301 AAAATATAAAAAATAAAG
1 AAAA-ATAAAAAATAAAG
526319 AAAAA
1 AAAAA
526324 GAAGGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 12 0.60
18 4 0.20
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAAATAAAAAATAAAG
Found at i:526493 original size:2 final size:2
Alignment explanation
Indices: 526486--526534 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
526476 GATAATTACA
526486 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
526527 AT AT AT AT
1 AT AT AT AT
526535 TAATAATACG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:528920 original size:29 final size:28
Alignment explanation
Indices: 528882--528960 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 28
528872 GAAAAAAAGC
*
528882 AAAGATAAAATAGTAAGTAAAAAA-ACAAAT
1 AAAGA-AAAATA-TAA-TAAAAAAGAAAAAT
*
528912 AAAGAAAAATATAAAAAATAAAGAAAAAT
1 AAAGAAAAATATAATAAA-AAAGAAAAAT
*
528941 AAGGAAAAATATAAATAAAA
1 AAAGAAAAATAT-AATAAAA
528961 CAAATAAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.07
28 6 0.14
29 23 0.55
30 10 0.24
ACGTcount: A:0.75, C:0.01, G:0.09, T:0.15
Consensus pattern (28 bp):
AAAGAAAAATATAATAAAAAAGAAAAAT
Found at i:528929 original size:10 final size:9
Alignment explanation
Indices: 528902--528979 Score: 54
Period size: 9 Copynumber: 8.6 Consensus size: 9
528892 TAGTAAGTAA
528902 AAAAACAAAT
1 AAAAA-AAAT
528912 AAAGAAAAAT
1 AAA-AAAAAT
*
528922 ATAAAAAAT
1 AAAAAAAAT
528931 AAAGAAAAAT
1 AAA-AAAAAT
*
528941 AAGGAAAAAT
1 AA-AAAAAAT
*
528951 ---ATAAAT
1 AAAAAAAAT
*
528957 AAAACAAAT
1 AAAAAAAAT
*
528966 AAACAAAAT
1 AAAAAAAAT
528975 AAAAA
1 AAAAA
528980 TAACAAAGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
6 5 0.09
9 24 0.44
10 23 0.43
11 2 0.04
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.13
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:528930 original size:9 final size:10
Alignment explanation
Indices: 528908--528953 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
528898 GTAAAAAAAC
*
528908 AAATAAAGAA
1 AAATATAGAA
528918 AAATATA-AA
1 AAATATAGAA
*
528927 AAATAAAGAA
1 AAATATAGAA
528937 AAATA-AGGAA
1 AAATATA-GAA
528947 AAATATA
1 AAATATA
528954 AATAAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 9 0.29
10 21 0.68
11 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (10 bp):
AAATATAGAA
Found at i:529049 original size:23 final size:23
Alignment explanation
Indices: 529002--529050 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
528992 AATAATATGT
*
529002 ATATATATATAATAAAAGAGTAA
1 ATATATATATAATAAAAGAGAAA
529025 ATATATATA-AATTAATAA-AGAAA
1 ATATATATATAA-TAA-AAGAGAAA
529048 ATA
1 ATA
529051 ATGAAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 2 0.09
23 19 0.83
24 2 0.09
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (23 bp):
ATATATATATAATAAAAGAGAAA
Found at i:529100 original size:25 final size:24
Alignment explanation
Indices: 529046--529100 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
529036 TTAATAAAGA
* *
529046 AAATAATGAAAAGAACATATATAC
1 AAATAATGAAAAAAAAATATATAC
*
529070 ATATAATGAAGAAAAAAATATA-ACC
1 AAATAATGAA-AAAAAAATATATA-C
529095 AAATAA
1 AAATAA
529101 AGATAATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.20
Consensus pattern (24 bp):
AAATAATGAAAAAAAAATATATAC
Found at i:530428 original size:5 final size:5
Alignment explanation
Indices: 530412--530449 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
530402 ATAAAATTAT
*
530412 ATATA TATATA ATATA ATATA ATATA A-ATA TTATA ATA
1 ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATA
530450 GTGAGGGTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
4 3 0.10
5 21 0.72
6 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:530446 original size:19 final size:20
Alignment explanation
Indices: 530409--530449 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
530399 TTAATAAAAT
*
530409 TATATATATATATAATATAA
1 TATATATATAAATAATATAA
*
530429 TATA-ATATAAATATTATAA
1 TATATATATAAATAATATAA
530448 TA
1 TA
530450 GTGAGGGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATATATATAAATAATATAA
Found at i:530556 original size:29 final size:29
Alignment explanation
Indices: 530512--530580 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 29
530502 AATTTTTTGA
*
530512 TTTTTT-A-TTTGAATCTC-TTTCCTCTT
1 TTTTTTGATTTTGAATCTCATTTCCTCCT
* *
530538 TTTTGTTGATTTTGTATCTCATTTTTCTCCT
1 TTTT-TTGATTTTGAATCTCA-TTTCCTCCT
530569 TTTTTTGATTTT
1 TTTTTTGATTTT
530581 TTTCTCATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
26 4 0.11
27 2 0.06
28 1 0.03
29 9 0.26
30 8 0.23
31 11 0.31
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.68
Consensus pattern (29 bp):
TTTTTTGATTTTGAATCTCATTTCCTCCT
Found at i:531087 original size:20 final size:20
Alignment explanation
Indices: 531062--531099 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
531052 TGTCAACACC
*
531062 TTTCCCTCTTTGCCCATTGG
1 TTTCCCACTTTGCCCATTGG
531082 TTTCCCACTTTGCCCATT
1 TTTCCCACTTTGCCCATT
531100 TGTGTGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.37, G:0.11, T:0.45
Consensus pattern (20 bp):
TTTCCCACTTTGCCCATTGG
Found at i:533201 original size:24 final size:24
Alignment explanation
Indices: 533173--533221 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
533163 CTCTTTTGAC
533173 TTTATTTTAGCTTACCTGAAGGAT
1 TTTATTTTAGCTTACCTGAAGGAT
533197 TTTATTTTAGCTTACCTGAAGGAT
1 TTTATTTTAGCTTACCTGAAGGAT
533221 T
1 T
533222 CATCTCATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.47
Consensus pattern (24 bp):
TTTATTTTAGCTTACCTGAAGGAT
Found at i:535439 original size:21 final size:20
Alignment explanation
Indices: 535399--535441 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
535389 GCTTAAATAA
*
535399 ATGTAATGCAGAATGCAAAT
1 ATGTAATGCAGAATGAAAAT
535419 ATGTAAATGCA-AATGTAAAAT
1 ATGT-AATGCAGAATG-AAAAT
535440 AT
1 AT
535442 ATTGATCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (20 bp):
ATGTAATGCAGAATGAAAAT
Found at i:537414 original size:19 final size:19
Alignment explanation
Indices: 537373--537425 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
537363 TTAAGTAAAT
**
537373 AAAAAAATACAAATAATTT
1 AAAAAAATACAAATAATAA
537392 AAAAAAATAACAAA-AATAA
1 AAAAAAAT-ACAAATAATAA
537411 AAAATAAATTACAAA
1 AAAA-AAA-TACAAA
537426 GGAATATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 15 0.52
20 13 0.45
21 1 0.03
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAAAATACAAATAATAA
Found at i:537553 original size:2 final size:2
Alignment explanation
Indices: 537542--537572 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
537532 ATGTACATAG
537542 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
537573 CACACACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:538488 original size:16 final size:17
Alignment explanation
Indices: 538467--538561 Score: 79
Period size: 16 Copynumber: 5.4 Consensus size: 17
538457 AAATTCAACT
*
538467 TAATAAGAAA-TAAATA
1 TAATAATAAATTAAATA
*
538483 TAATAATAATATTAATTAA
1 TAATAATAA-ATTAAAT-A
*
538502 TAATATTAATTATTAAATA
1 TAATAATAA--ATTAAATA
538521 TAATAA-ATAATTAAAATA
1 TAATAATA-AATT-AAATA
538539 TAATAATAAA-TAAATA
1 TAATAATAAATTAAATA
*
538555 TAGTAAT
1 TAATAAT
538562 TCAAAATATA
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
16 19 0.29
17 5 0.08
18 18 0.27
19 17 0.26
20 7 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TAATAATAAATTAAATA
Found at i:538502 original size:13 final size:13
Alignment explanation
Indices: 538486--538531 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
538476 ATAAATATAA
538486 TAATAATATTAAT
1 TAATAATATTAAT
538499 TAATAATATTAAT
1 TAATAATATTAAT
*
538512 TATTAA-ATATAAT
1 TAATAATAT-TAAT
*
538525 AAATAAT
1 TAATAAT
538532 TAAAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 2 0.07
13 26 0.93
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATAATATTAAT
Found at i:538671 original size:21 final size:18
Alignment explanation
Indices: 538635--538673 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 18
538625 ATTATATGTA
538635 TAATATATTAAATATAAT
1 TAATATATTAAATATAAT
538653 TAATAATATTATAATTATAAT
1 TAAT-ATATTA-AA-TATAAT
538674 ATATTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 2 0.11
21 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATATTAAATATAAT
Found at i:539127 original size:15 final size:14
Alignment explanation
Indices: 539083--539130 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
539073 AATTCCAAAA
*
539083 TATATTATAATTAT
1 TATATTTTAATTAT
*
539097 AATATTATTAATTAT
1 TATATT-TTAATTAT
539112 TATATTTTAATATAT
1 TATATTTTAAT-TAT
539127 TATA
1 TATA
539131 CATATAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATATTTTAATTAT
Found at i:539229 original size:12 final size:13
Alignment explanation
Indices: 539160--539270 Score: 50
Period size: 15 Copynumber: 8.0 Consensus size: 13
539150 CAAATTTACA
539160 AATTATA-TTA-T
1 AATTATATTTATT
*
539171 AATTATTATTTATA
1 AATTA-TATTTATT
* *
539185 AAATATCTATT-TT
1 AATTATAT-TTATT
539198 AATACTATATTTATT
1 AAT--TATATTTATT
*
539213 TATTATATTT-TT
1 AATTATATTTATT
539225 AATTATATTATATTT
1 AATTATATT-TA-TT
*
539240 AATATTTAATATTATT
1 AAT-TAT-AT-TTATT
539256 ATTATTATATTTATT
1 A--ATTATATTTATT
539271 TATTGTGTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
11 5 0.07
12 12 0.16
13 16 0.21
14 8 0.11
15 18 0.24
16 7 0.09
17 6 0.08
18 3 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (13 bp):
AATTATATTTATT
Found at i:539247 original size:22 final size:21
Alignment explanation
Indices: 539208--539273 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
539198 AATACTATAT
*
539208 TTAT-TTATTA-TATTTTTAA
1 TTATATTATTATTATATTTAA
539227 TTATATTA-TATTTAATATTTAA
1 TTATATTATTA-TT-ATATTTAA
*
539249 -TATTATTATTATTATATTTAT
1 TTA-TATTATTATTATATTTAA
539270 TTAT
1 TTAT
539274 TGTGTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
19 6 0.16
20 3 0.08
21 11 0.29
22 16 0.42
23 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATATTATTATTATATTTAA
Found at i:539263 original size:33 final size:32
Alignment explanation
Indices: 539209--539272 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
539199 ATACTATATT
* *
539209 TATTTATTATATTTTTAATTATATTATATTTAA
1 TATTTAATATATTATTAATTATATT-TATTTAA
539242 TATTTAATATTATTATT-ATTATATTTATTTA
1 TATTTAATA-TATTATTAATTATATTTATTTA
539273 TTGTGTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 6 0.21
33 16 0.57
34 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (32 bp):
TATTTAATATATTATTAATTATATTTATTTAA
Found at i:540060 original size:62 final size:62
Alignment explanation
Indices: 539989--540105 Score: 234
Period size: 62 Copynumber: 1.9 Consensus size: 62
539979 TCGTCATGCA
539989 CTCCTGCTCCTCGCGTGATTCCTCTTGCAGCTGCTCAGGAGACCTCATGCATGCACCTATTC
1 CTCCTGCTCCTCGCGTGATTCCTCTTGCAGCTGCTCAGGAGACCTCATGCATGCACCTATTC
540051 CTCCTGCTCCTCGCGTGATTCCTCTTGCAGCTGCTCAGGAGACCTCATGCATGCA
1 CTCCTGCTCCTCGCGTGATTCCTCTTGCAGCTGCTCAGGAGACCTCATGCATGCA
540106 GCTGTAATAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.15, C:0.37, G:0.21, T:0.28
Consensus pattern (62 bp):
CTCCTGCTCCTCGCGTGATTCCTCTTGCAGCTGCTCAGGAGACCTCATGCATGCACCTATTC
Found at i:540601 original size:21 final size:21
Alignment explanation
Indices: 540576--540619 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
540566 AATTTAGTTA
540576 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
540597 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
540618 AT
1 AT
540620 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:540633 original size:28 final size:28
Alignment explanation
Indices: 540596--540649 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
540586 TAGTATAAAT
*
540596 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
540624 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
540650 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:540732 original size:44 final size:49
Alignment explanation
Indices: 540625--540732 Score: 129
Period size: 50 Copynumber: 2.3 Consensus size: 49
540615 GTTATATTAT
540625 ATTAATTTGTTAGTTTAAGTTATATATTAGATTATATAAAAAATTAGTTA
1 ATTAATTTGTTAGTTTAAGTTATATA-TAGATTATATAAAAAATTAGTTA
* * *
540675 ATTAGTTTCTTAGTTTAAGTTAT-TA-A-ATGTA-A-AAAAAA-TATTTA
1 ATTAATTTGTTAGTTTAAGTTATATATAGAT-TATATAAAAAATTAGTTA
540719 ATTAATTTGTTAGT
1 ATTAATTTGTTAGT
540733 GTGTTTAAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
44 17 0.33
45 6 0.12
46 3 0.06
47 3 0.06
49 2 0.04
50 21 0.40
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (49 bp):
ATTAATTTGTTAGTTTAAGTTATATATAGATTATATAAAAAATTAGTTA
Found at i:541202 original size:83 final size:84
Alignment explanation
Indices: 541109--541269 Score: 272
Period size: 83 Copynumber: 1.9 Consensus size: 84
541099 AGTTAGTTAG
541109 TTTATATTAGAGTATATAAAATTAATTTGTTTAATTTATTTCC-GTTT-AAAAAAATATTGTGTT
1 TTTATATTAGAGTATATAAAATTAATTTGTTTAATTTA-TTCCAGTTTAAAAAAAATATTGTGTT
* *
541172 TACAAATATTTAGTATTTAT
65 AAAAAATATTTAGTATTTAT
*
541192 TTTATATTAGATTATATAAAATTAATTTGTTTAATTTATTCCAGTTTAAAAAAAATATTGTGTTA
1 TTTATATTAGAGTATATAAAATTAATTTGTTTAATTTATTCCAGTTTAAAAAAAATATTGTGTTA
541257 AAAAATATTTAGT
66 AAAAATATTTAGT
541270 GTCAAACCAT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
82 4 0.05
83 41 0.56
84 28 0.38
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (84 bp):
TTTATATTAGAGTATATAAAATTAATTTGTTTAATTTATTCCAGTTTAAAAAAAATATTGTGTTA
AAAAATATTTAGTATTTAT
Found at i:542955 original size:63 final size:63
Alignment explanation
Indices: 542888--543006 Score: 229
Period size: 63 Copynumber: 1.9 Consensus size: 63
542878 AATAATTATT
542888 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATAATTTGG
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATAATTTGG
*
542951 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGGTAGTAAT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
543007 GATTAGTAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (63 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATAATTTGG
Found at i:542964 original size:24 final size:24
Alignment explanation
Indices: 542937--543019 Score: 73
Period size: 24 Copynumber: 3.4 Consensus size: 24
542927 AATGATTTGA
542937 TAGTAATAATTTGGTAGTAATGAT
1 TAGTAATAATTTGGTAGTAATGAT
** *
542961 TAGTAATAATGAAATTATTATTAAT-AT
1 TAGTAATAAT----TTGGTAGTAATGAT
*
542988 T--TAATGATTTGGTAGTAATGAT
1 TAGTAATAATTTGGTAGTAATGAT
543010 TAGTAATAAT
1 TAGTAATAAT
543020 GAAATTATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
21 8 0.18
22 3 0.07
24 16 0.36
25 6 0.14
27 3 0.07
28 8 0.18
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (24 bp):
TAGTAATAATTTGGTAGTAATGAT
Found at i:543000 original size:49 final size:49
Alignment explanation
Indices: 542940--543066 Score: 218
Period size: 49 Copynumber: 2.6 Consensus size: 49
542930 GATTTGATAG
542940 TAATAATTTGGTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATAATTTGGTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
542989 TAATGATTTGGTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATAATTTGGTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
* *
543038 TAATTATTTGATAGTAATGATTTAGTAAT
1 TAATAATTTGGTAGTAATGA-TTAGTAAT
543067 TATTAGTAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
49 66 0.89
50 8 0.11
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (49 bp):
TAATAATTTGGTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:543019 original size:112 final size:113
Alignment explanation
Indices: 542815--543087 Score: 364
Period size: 112 Copynumber: 2.4 Consensus size: 113
542805 TAATAATGAT
* * *
542815 ATGATTTGATTTAGTAATGATTTGCTAATCATGATT--TAATAATGAATTTA-TATTTAAAATTA
1 ATGATTTGA--TAGTAATGATTTG-TAGTAATGATTAGTAATAATGAAATTATTATTTAAAATTA
*
542877 TAATAATTATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTA
63 TAATAATTATGTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTA
* *
542928 ATGATTTGATAGTAATAATTTGGTAGTAATGATTAGTAATAATGAAATTATTA-TTAATATT-TA
1 ATGATTTGATAGTAATGATTT-GTAGTAATGATTAGTAATAATGAAATTATTATTTAAAATTATA
*
542991 ATGATT-TGGTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTA
65 ATAATTAT-GTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTA
* *
543040 ATTATTTGATAGTAATGA-TT-TAGTAATTATTAGTAATAATGAAATTAT
1 ATGATTTGATAGTAATGATTTGTAGTAATGATTAGTAATAATGAAATTAT
543088 AATAATAATT
Statistics
Matches: 145, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
109 27 0.19
111 23 0.16
112 64 0.44
113 29 0.20
114 2 0.01
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (113 bp):
ATGATTTGATAGTAATGATTTGTAGTAATGATTAGTAATAATGAAATTATTATTTAAAATTATAA
TAATTATGTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTA
Found at i:543044 original size:63 final size:62
Alignment explanation
Indices: 542896--543095 Score: 198
Period size: 63 Copynumber: 3.2 Consensus size: 62
542886 TTTAGTAATG
* * *
542896 ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATAATTTGGTAGTAATG--
1 ATTATTAATAAT-AAATTATTATTAATATTTAATGATTTG-TAGTAATAA-TTAGTAATAATGAA
* *
542959 ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGGTAGTAATGATTAGTAATAATGAA
1 ATTATTAATAAT-AAATTATTATTAATATTTAATGATTT-GTAGTAATAATTAGTAATAATGAA
* * * * *
543023 ATTATTATTAAT-ATTTAATTATTTGATA-GTAATGA-TT-TAGTAATTATTAGTAATAATGAA
1 ATTATTAATAATAAATT-ATTA-TTAATATTTAATGATTTGTAGTAATAATTAGTAATAATGAA
543083 ATTA-TAATAATAA
1 ATTATTAATAATAA
543096 TTTGATACTA
Statistics
Matches: 121, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
59 6 0.05
60 27 0.22
62 15 0.12
63 57 0.47
64 16 0.13
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (62 bp):
ATTATTAATAATAAATTATTATTAATATTTAATGATTTGTAGTAATAATTAGTAATAATGAA
Found at i:543301 original size:19 final size:18
Alignment explanation
Indices: 543277--543368 Score: 61
Period size: 19 Copynumber: 5.2 Consensus size: 18
543267 CATAAAAACG
543277 ATTTAATAATGATTTTAAT
1 ATTT-ATAATGATTTTAAT
*
543296 A-TT-TAATGA-TTTGAT
1 ATTTATAATGATTTTAAT
* *
543311 GATTTAGTCATTATTTTAAT
1 -ATTTA-TAATGATTTTAAT
*
543331 A-TT-TAATGA-TTTGAT
1 ATTTATAATGATTTTAAT
543346 GATTTAGTAATGATTTTAAT
1 -ATTTA-TAATGATTTTAAT
543366 ATT
1 ATT
543369 ATGATTTAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
15 10 0.18
16 12 0.22
17 4 0.07
18 4 0.07
19 15 0.27
20 10 0.18
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.53
Consensus pattern (18 bp):
ATTTATAATGATTTTAAT
Found at i:543304 original size:16 final size:15
Alignment explanation
Indices: 543283--543379 Score: 54
Period size: 16 Copynumber: 5.9 Consensus size: 15
543273 AACGATTTAA
543283 TAATGATTTTAATATT
1 TAATGA-TTTAATATT
*
543299 TAATGATTTGATGATT
1 TAATGATTTAAT-ATT
*
543315 TAGTCATTATTTTAATATT
1 TA---ATGA-TTTAATATT
*
543334 TAATGATTTGATGATTT
1 TAATGATTTAAT-A-TT
543351 AGTAATGATTTTAATA-T
1 --TAATGA-TTTAATATT
543368 T-ATGATTTAATA
1 TAATGATTTAATA
543380 ATGATTTAGT
Statistics
Matches: 65, Mismatches: 6, Indels: 23
0.69 0.06 0.24
Matches are distributed among these distances:
13 7 0.11
14 4 0.06
15 11 0.17
16 15 0.23
17 3 0.05
19 15 0.23
20 10 0.15
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.53
Consensus pattern (15 bp):
TAATGATTTAATATT
Found at i:543307 original size:8 final size:8
Alignment explanation
Indices: 543283--543351 Score: 52
Period size: 8 Copynumber: 8.2 Consensus size: 8
543273 AACGATTTAA
543283 TAATGATTT
1 TAATGA-TT
543292 TAAT-ATT
1 TAATGATT
543299 TAATGATT
1 TAATGATT
*
543307 TGATGATT
1 TAATGATT
*
543315 TAGTCATTATTT
1 TA---ATGA-TT
543327 TAAT-ATT
1 TAATGATT
543334 TAATGATT
1 TAATGATT
*
543342 TGATGATT
1 TAATGATT
543350 TA
1 TA
543352 GTAATGATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
7 12 0.24
8 24 0.49
9 6 0.12
11 3 0.06
12 4 0.08
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (8 bp):
TAATGATT
Found at i:543316 original size:35 final size:35
Alignment explanation
Indices: 543276--543375 Score: 159
Period size: 35 Copynumber: 2.9 Consensus size: 35
543266 CCATAAAAAC
*
543276 GATTTAATAATGATTTTAATATTTAATGATTTGAT
1 GATTTAGTAATGATTTTAATATTTAATGATTTGAT
* *
543311 GATTTAGTCATTATTTTAATATTTAATGATTTGAT
1 GATTTAGTAATGATTTTAATATTTAATGATTTGAT
543346 GATTTAGTAATGATTTTAATA-TT-ATGATTT
1 GATTTAGTAATGATTTTAATATTTAATGATTT
543376 AATAATGATT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 7 0.12
34 2 0.03
35 51 0.85
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (35 bp):
GATTTAGTAATGATTTTAATATTTAATGATTTGAT
Found at i:543483 original size:98 final size:98
Alignment explanation
Indices: 543369--543730 Score: 475
Period size: 98 Copynumber: 3.7 Consensus size: 98
543359 TTTTAATATT
543369 ATGATTTAATAATGATTT-AGTAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAA
1 ATGATTTAATAATGATTTGA-TAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAA
543433 TGATTTAATAATGATTTTAATATTTAATGATTTG
65 TGATTTAATAATGATTTTAATATTTAATGATTTG
*
543467 ATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAAT
1 ATGATTTAATAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAAT
*
543532 GATTTAAAAATGATTTTAATATTTAATGATTTG
66 GATTTAATAATGATTTTAATATTTAATGATTTG
* * * *
543565 ATGATTTAGTAGTGATTTGATAATAACCATTATAATAATGATTTAGCAATAATCATTATAATAAT
1 ATGATTTAATAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAAT
* * *
543630 GATTTAATAATAATCATT-ATA-ATAATGATTTACTAG
66 GATTTAATAATGAT-TTTAATATTTAATGA-TT--T-G
* * * * *
543666 TAATGATTTAATAATGATTT-AGTAATGAT-TTTATAATAATGATTTAATACTAATGATT-TAAT
1 --ATGATTTAATAATGATTTGA-TAATAATCATTATAATAATGATTTAGTAATAATCATTATAAT
543728 AAT
63 AAT
543731 TATTACTAAT
Statistics
Matches: 237, Mismatches: 18, Indels: 15
0.88 0.07 0.06
Matches are distributed among these distances:
97 6 0.03
98 173 0.73
99 3 0.01
100 1 0.00
101 8 0.03
102 25 0.11
103 21 0.09
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (98 bp):
ATGATTTAATAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAAT
GATTTAATAATGATTTTAATATTTAATGATTTG
Found at i:543505 original size:26 final size:25
Alignment explanation
Indices: 543353--543743 Score: 288
Period size: 26 Copynumber: 15.7 Consensus size: 25
543343 GATGATTTAG
*
543353 TAATGATTT-TAATATTATGATT-TAA
1 TAATGATTTATAATA--ATCATTATAA
543378 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTA-TAATAATCATTATAA
543404 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTA-TAATAATCATTATAA
* *
543430 TAATGA-TT-TAATAATGATTTTAA
1 TAATGATTTATAATAATCATTATAA
* * * * * * * *
543453 TATTTAATGAT-TTGATGATT-TAG
1 TAATGATTTATAATAATCATTATAA
543476 TAATGATTTGATAATAATCATTATAA
1 TAATGATTT-ATAATAATCATTATAA
543502 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTA-TAATAATCATTATAA
* *
543528 TAATGATTTA-AA-AATGATTTTAA
1 TAATGATTTATAATAATCATTATAA
* * * * * * * *
543551 TATTTAATGAT-TTGATGATT-TAG
1 TAATGATTTATAATAATCATTATAA
* *
543574 TAGTGATTTGATAATAACCATTATAA
1 TAATGATTT-ATAATAATCATTATAA
*
543600 TAATGATTTAGCAATAATCATTATAA
1 TAATGATTTA-TAATAATCATTATAA
543626 TAATGATTTAATAATAATCATTATAA
1 TAATGATTT-ATAATAATCATTATAA
* *
543652 TAATGATTTACTAGTAATGATT-TAA
1 TAATGATTTA-TAATAATCATTATAA
* *
543677 TAATGATTTAGTAATGAT-TTTATAA
1 TAATGATTTA-TAATAATCATTATAA
* *
543702 TAATGATTTAATACTAATGATT-TAA
1 TAATGATTT-ATAATAATCATTATAA
*
543727 TAATTA-TTACTAATAAT
1 TAATGATTTA-TAATAAT
543744 TATGGAATAA
Statistics
Matches: 295, Mismatches: 50, Indels: 43
0.76 0.13 0.11
Matches are distributed among these distances:
23 47 0.16
24 30 0.10
25 74 0.25
26 138 0.47
27 6 0.02
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (25 bp):
TAATGATTTATAATAATCATTATAA
Found at i:543639 original size:11 final size:11
Alignment explanation
Indices: 543597--543730 Score: 88
Period size: 14 Copynumber: 10.6 Consensus size: 11
543587 ATAACCATTA
543597 TAATAATGATT
1 TAATAATGATT
*
543608 TAGCAATAATCATT
1 T---AATAATGATT
543622 ATAATAATGATTT
1 -TAATAATGA-TT
*
543635 AATAATAATCATT
1 --TAATAATGATT
543648 ATAATAATGATT
1 -TAATAATGATT
543660 TACTAGTAATGATT
1 TA--A-TAATGATT
543674 TAATAATGATT
1 TAATAATGATT
*
543685 TAGTAATGATTTT
1 TAATAATGA--TT
543698 ATAATAATGATT
1 -TAATAATGATT
543710 TAATACTAATGATT
1 T-A-A-TAATGATT
543724 TAATAAT
1 TAATAAT
543731 TATTACTAAT
Statistics
Matches: 102, Mismatches: 6, Indels: 30
0.74 0.04 0.22
Matches are distributed among these distances:
11 24 0.24
12 23 0.23
13 9 0.09
14 45 0.44
15 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (11 bp):
TAATAATGATT
Found at i:543894 original size:24 final size:24
Alignment explanation
Indices: 543846--543890 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
543836 GATTTGATAC
*
543846 TAATGATTTACTAATTATTATTAA
1 TAATGATTTACTAATTAATATTAA
*
543870 TAATGATTTA-TTATTAATATT
1 TAATGATTTACTAATTAATATT
543891 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATGATTTACTAATTAATATTAA
Found at i:543897 original size:17 final size:17
Alignment explanation
Indices: 543857--543898 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
543847 AATGATTTAC
543857 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
543874 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
543891 TAATTATT
1 TAATTATT
543899 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:544893 original size:23 final size:23
Alignment explanation
Indices: 544863--544907 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
544853 CTCCAATTAA
*
544863 AAATAATAAAATTGATTTAAATC
1 AAATAATAAAATTAATTTAAATC
* *
544886 AAATAATATAGTTAATTTAAAT
1 AAATAATAAAATTAATTTAAAT
544908 AATAATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
AAATAATAAAATTAATTTAAATC
Found at i:546151 original size:15 final size:16
Alignment explanation
Indices: 546131--546164 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
546121 CAAAAAAATT
546131 TAATATAAT-AACTTA
1 TAATATAATAAACTTA
546146 TAATATAATAAACTTA
1 TAATATAATAAACTTA
546162 TAA
1 TAA
546165 CGTAACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATAATAAACTTA
Found at i:546254 original size:30 final size:32
Alignment explanation
Indices: 546216--546291 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 32
546206 TTTCCCTTAA
546216 ACAACTAATAAACTATTCTTTAA-TATAACTT
1 ACAACTAATAAACTATTCTTTAATTATAACTT
* * *
546247 A-AACTAATAAACGATTTTTTAATTATAATTT
1 ACAACTAATAAACTATTCTTTAATTATAACTT
*
546278 ACTACTAA-AAACTA
1 ACAACTAATAAACTA
546292 ATTAACTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
30 19 0.50
31 14 0.37
32 5 0.13
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.38
Consensus pattern (32 bp):
ACAACTAATAAACTATTCTTTAATTATAACTT
Found at i:546805 original size:22 final size:22
Alignment explanation
Indices: 546779--546853 Score: 123
Period size: 22 Copynumber: 3.4 Consensus size: 22
546769 ATGAAGCAAC
546779 GGGAGCAGGCGAGCATGCAATG
1 GGGAGCAGGCGAGCATGCAATG
546801 GGGAGCAGGCGAGCATGCAATG
1 GGGAGCAGGCGAGCATGCAATG
* **
546823 GGGAGCAGGTGAGCATGCAGCG
1 GGGAGCAGGCGAGCATGCAATG
546845 GGGAGCAGG
1 GGGAGCAGG
546854 GCGCAGGACA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.25, C:0.17, G:0.49, T:0.08
Consensus pattern (22 bp):
GGGAGCAGGCGAGCATGCAATG
Found at i:546979 original size:10 final size:10
Alignment explanation
Indices: 546964--547073 Score: 60
Period size: 10 Copynumber: 10.1 Consensus size: 10
546954 CCTATCCTTG
546964 CTCGGATGCC
1 CTCGGATGCC
546974 CTCGGATG-C
1 CTCGGATGCC
*
546983 CTCGCATAGCTC
1 CTCGGAT-GC-C
546995 GCTCGGATGGCC
1 -CTCGGAT-GCC
*
547007 TCGGTCGGATGCG
1 -C--TCGGATGCC
*
547020 CTCGGATGGC
1 CTCGGATGCC
*
547030 CTCGGATGCT
1 CTCGGATGCC
*
547040 CTCGCATAGCTC
1 CTCGGAT-GC-C
* *
547052 GCCCGGATGGC
1 -CTCGGATGCC
547063 CTCGGATGCC
1 CTCGGATGCC
547073 C
1 C
547074 AGCGTGTTGG
Statistics
Matches: 75, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
9 7 0.09
10 39 0.52
11 3 0.04
12 5 0.07
13 15 0.20
14 6 0.08
ACGTcount: A:0.11, C:0.35, G:0.33, T:0.21
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:549518 original size:2 final size:2
Alignment explanation
Indices: 549511--549546 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
549501 TAATAAATGC
549511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
549547 TCTAAAGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.